Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


Navigation/Query Panel:
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final measured Gene Rank expected Hugo description
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
final
measured
Rank
expected
Hugo
description
0.202699899 0.153382 2756 0.756695 ATAD1
0.203634998 0.303744 2755 1.49161 SSU72
0.203655769 0.429899 2754 2.11091 ETFB ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT (BETA-ETF). [SWISSPROT;Acc:P38117]
0.203807089 0.099187 2753 0.486671 PGAM5
0.203931468 0.117541 2751 0.576375 NARS2
2752 NARS "ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.22) (ASPARAGINE-- TRNA LIGASE) (ASNRS). [SWISSPROT;Acc:O43776]"
0.203998273 0.382713 2750 1.87606 ERCC2 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX HELICASE SUBUNIT (EC 3.6.1.-) (DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS) (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (CXPD) (DNA EXCISION REPAIR PROTEIN ERCC-2). [SWISSPROT;Acc:P18074]
0.204203283 0.334146 2748 1.63634 WDR33 WD-REPEAT PROTEIN WDC146. [SWISSPROT;Acc:Q9C0J8]
2749 CPSF1 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]"
0.204415918 0.116023 2747 0.567583 OTUB2 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 2. [RefSeq;Acc:NM_023112]
0.204511641 0.0555879 2746 0.271808 GCLM GLUTAMATE--CYSTEINE LIGASE REGULATORY SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS LIGHT CHAIN) (GLUTAMATE--CYSTEINE LIGASE MODIFIER SUBUNIT). [SWISSPROT;Acc:P48507]
0.204511763 0.0833819 2745 0.407712 PPCS
0.204512008 0.027794 2743 0.135904 GCLC GLUTAMATE--CYSTEINE LIGASE CATALYTIC SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS HEAVY CHAIN). [SWISSPROT;Acc:P48506]
0.111176 2744 0.543616 PPCDC
0.204820879 0.0289586 2742 0.141385 KIAA1012 TRS85 HOMOLOG. [SWISSPROT;Acc:Q9Y2L5]
0.204821697 0.364089 2741 1.77759 CPSF4 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 4, 30KD SUBUNIT; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR, 30KD; NO ARCHES-LIKE (ZEBRAFISH) ZINC FINGER PROTEIN; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR. [RefSeq;Acc:NM_006693]"
0.205155373 0.366149 2740 1.78474 CPSF2 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q9P2I0]"
0.205329641 0.0252114 2737 0.122785 VAMP2 VESICLE-ASSOCIATED MEMBRANE PROTEIN 2 (VAMP-2) (SYNAPTOBREVIN 2). [SWISSPROT;Acc:P19065]
2738 TMEM64
2739 VAMP4 VESICULE-ASSOCIATED MEMBRANE PROTEIN 4 (VAMP-4). [SWISSPROT;Acc:O75379]
0.205330288 0.387487 2736 1.88714 CDIPT CDP-DIACYLGLYCEROL--INOSITOL 3-PHOSPHATIDYLTRANSFERASE (EC 2.7.8.11) (PHOSPHATIDYLINOSITOL SYNTHASE) (PTDINS SYNTHASE) (PI SYNTHASE). [SWISSPROT;Acc:O14735]
0.205330688 0.0215242 2735 0.104827 VAMP3 VESICLE-ASSOCIATED MEMBRANE PROTEIN 3 (VAMP-3) (SYNAPTOBREVIN 3) (CELLUBREVIN) (CEB). [SWISSPROT;Acc:Q15836]
0.205330704 0.0233268 2734 0.113606 VAMP1 VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (VAMP-1) (SYNAPTOBREVIN 1). [SWISSPROT;Acc:P23763]
0.205330819 0.145697 2733 0.709572 ARFGAP1 ADP-RIBOSYLATION FACTOR GTPASE ACTIVATING PROTEIN 1 (ADP-RIBOSYLATION FACTOR 1 GTPASE ACTIVATING PROTEIN) (ARF1 GAP) (ARF1-DIRECTED GTPASE- ACTIVATING PROTEIN) (GAP PROTEIN). [SWISSPROT;Acc:Q8N6T3]
0.205477774 0.241572 2732 1.17566 SRP54 SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54). [SWISSPROT;Acc:P13624]
0.205675743 0.354332 2731 1.72277 CRLS1
0.205687337 0.087666 2730 0.42621 CCBL2
0.205692245 0.0967095 2729 0.470166 GPT ALANINE AMINOTRANSFERASE (EC 2.6.1.2) (GLUTAMIC--PYRUVIC TRANSAMINASE) (GPT) (GLUTAMIC--ALANINE TRANSAMINASE). [SWISSPROT;Acc:P24298]
0.205698985 0.113234 2727 0.550484 CCBL1 CYTOPLASMIC CYSTEINE CONJUGATE-BETA LYASE; GLUTAMINE-PHENYLPYRUVATE AMINOTRANSFERASE. [RefSeq;Acc:NM_004059]
2728 GPT2 ALANINE AMINOTRANSFERASE 2; GLUTAMIC-PYRUVATE TRANSAMINASE 2. [RefSeq;Acc:NM_133443]
0.20572819 0.462047 2726 2.24591 FHL5 ACTIVATOR OF CAMP-RESPONSIVE ELEMENT MODULATOR (CREM) IN TESTIS; LIM PROTEIN ACT. [RefSeq;Acc:NM_020482]
0.205845886 0.10808 2725 0.525053 no value
0.206199422 0.398002 2724 1.93018 ISL1 INSULIN GENE ENHANCER PROTEIN ISL-1 (ISLET-1). [SWISSPROT;Acc:P20663]
0.206548387 0.0313747 2723 0.1519 no value
0.206548442 0.754507 2722 3.65293 PCNA PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (CYCLIN). [SWISSPROT;Acc:P12004]
0.206712814 0.0767473 2721 0.371275 NDUFA12 NADH-UBIQUINONE OXIDOREDUCTASE SUBUNIT B17.2 (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B17.2) (CI-B17.2) (CIB17.2) (13 KDA DIFFERENTIATION-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9UI09]
0.206845844 0.10212 2720 0.493701 MCTP1
0.206933959 0.0784199 2719 0.378961 MCTP2
0.207333004 0.0926594 2718 0.446911 ABHD14A
0.207334011 0.416194 2717 2.00736 SLC27A4 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 4; FATTY ACID TRANSPORT PROTEIN 4. [RefSeq;Acc:NM_005094]"
0.207336421 0.411399 2716 1.98421 no value
0.207339211 0.439273 2715 2.11862 SLC27A3 SOLUTE CARRIER FAMILY 27 MEMBER 3; FATTY ACID TRANSPORT PROTEIN 3. [RefSeq;Acc:NM_024330]
0.207340198 0.44721 2714 2.15689 SLC27A5 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5; VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 2; VERY LONG-CHAIN ACYL-COA SYNTHETASE-RELATED PROTEIN; LIKELY ORTHOLOG OF MOUSE SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5. ["
0.207342426 0.0244747 2713 0.11804 LBR LAMIN B RECEPTOR (INTEGRAL NUCLEAR ENVELOPE INNER MEMBRANE PROTEIN) (LMN2R). [SWISSPROT;Acc:Q14739]
0.207342721 0.0196287 2712 0.0946679 TM7SF2 DELTA(14)-STEROL REDUCTASE (EC 1.3.1.70) (C-14 STEROL REDUCTASE) (STEROL C14-REDUCTASE) (DELTA14-SR) (TRANSMEMBRANE 7 SUPERFAMILY MEMBER 2) (ANOTHER NEW GENE 1) (PUTATIVE STEROL REDUCTASE SR-1). [SWISSPROT;Acc:O76062]
0.207342829 0.46044 2711 2.22067 SLC27A6 VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 1. [RefSeq;Acc:NM_014031]
0.207343546 0.144805 2710 0.698382 UTP3 DISRUPTER OF SILENCING 10. [RefSeq;Acc:NM_020368]
0.207346964 0.465778 2709 2.24637 DIP2B SIMILAR TO CG7020 GENE PRODUCT (FRAGMENT). [SPTREMBL;Acc:Q96IB4]
0.207355944 0.553489 2708 2.66927 SLC27A2 VERY-LONG-CHAIN ACYL-COA SYNTHETASE (EC 6.2.1.-) (VERY-LONG-CHAIN- FATTY-ACID-COA LIGASE). [SWISSPROT;Acc:O14975]
0.207358653 0.542979 2707 2.61855 no value

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/